Closed mostafaalishahi closed 8 months ago
Hi, I need to check this, I haven't used the OMOP formatted data lately. Writing to OMOP should take a long time, but not that long.
In the meantime, the BlendedICU data can be used in its original form with medications and timeseries as patient-level parquet files located in blended_data/formatted_medications/
and blended_data/formatted_timeseries/
and labels/flat data in blended_data/preprocessed_labels.parquet
and blended_data/preprocessed_flat.parquet
.
Thanks again for the feedback, getting back to you soon.
Hi, could you please tell me if this is normal that I am getting 1890 out of 100 chunks? what X refers to in X/100 chunks print out line.
Thanks,
Hi, There were several issues introduced by "quick changes" made during reviewing process. I'm done fixing them and now this step runs in ~10hours. I will push the changes tomorrow.
Thank you for your patience, Getting back to you (very) soon
Hi I did test it on my side, it runs with v0.1.5.
You have to start 4_write_OMOP from chunk 0, there will actually be 100 chunks now.
Note that measurement_table
and drug_exposure_table
can be launched in parallel for a slight speedup.
Many thanks.
Hi again, I am wondering how long this script (4_write_omop.py) would take to run (took me more than 24 hours) and it resulted into the following error after 24 hours appreciate any feedbacks to avoid rerunning the script and get it running from where it left off. What would chunk X/100 mean here. Is it normal that I got 1890 out of 100 chunks?